Fully cook the bacon to render the fat. Remove the bacon pieces and reserve the piece for garnish.
Add one minced onion to the bacon fat, and saute until translucent , but not browned. If you want a thicker chowder, add 2 Tbsp flour to this mixture, stir in, and cook for about a minute or so.
Add clam juice, and diced potatoes. Cook for approx. 10 minutes or until potatoes are tender but not mushy.
Temper (warm) the milk and cream with some of the hot liquid mixture. Then add the milk and cream to the chowder. Cook on low another 5 minutes or cook until the potatoes are tender. Add clams, haddock, and scallops.
Add thyme, salt and pepper and bay leaf.
Cook on low for 10 to 15 minutes or so, until fish is cooked.